in reply to Random shuffling

Looks fine to me, but the best way would be to verify it yourself, print out the before & after sequences below each other and change the window size to something readable (e.g. 5).

That said, I think the problem maybe miss-represented, are you sure you dont want to break up the DNA into window-sized chunks and shuffle the chunks? This would be a more useful exercise!

Update: ...SO VERY different from what has been published
It would be nice to see a link to the published work!

This is not a Signature...

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Re^2: Random shuffling
by onlyIDleft (Scribe) on Jun 20, 2015 at 18:31 UTC

    Yeah, I've done that already, since that is the easiest thing to do. It behaves as expected for mock input files.

    Like I said in my first post, I dont want to assume I am 100% right, when I might be claiming that results in a paper from the lab of an established big wig in my field are incorrect / falsified! :(

    But now, thanks to all your inputs, I know there is no fatal error in logic for this step. So thank you all!